Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008617.1 Kokia drynarioides strain JFW-HI SEQ_123296, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 12002
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:389 original size:87 final size:85
Alignment explanation
Indices: 229--513 Score: 283
Period size: 87 Copynumber: 3.3 Consensus size: 85
219 TTTTGGATAC
* * * **
229 TTAGGGGCAAAATGATAATTTTTGGATGATT-G-GGGCAAAATGGTAATTTTTGGATGCTCGGGG
1 TTAGGGTCAAAATG-TAATTTTTGGATG-TTCGAGGGCAAAAT-GTAATTTTTGGAAGTTTAGGG
*
292 GCAAAATGGTAATTTTGAAAAGT
63 GTAAAATGGTAATTTTGAAAAGT
*
315 TTAGGGTCAAAATGGTAATTTTTGGATGTTCGAGGGCAAAAATGTGATTTTTGGAAGTTTAGGGG
1 TTAGGGTCAAAAT-GTAATTTTTGGATGTTCGAGGGC-AAAATGTAATTTTTGGAAGTTTAGGGG
*
380 TAAAATGGTAATTTTTGGAAAGT
64 TAAAATGGTAA-TTTTGAAAAGT
* * * * *
403 TCATGGTCAAAATGTAA-GTTTGTGAAGTTC-AGGGTCAAAATGTAATTTTTAGAAAGTTTAGGG
1 TTAGGGTCAAAATGTAATTTTTG-GATGTTCGAGGG-CAAAATGTAATTTTT-GGAAGTTTAGGG
* **
466 GTCAAAAT-GTATTTTTTTTAAAGT
63 GT-AAAATGGTA-ATTTTGAAAAGT
490 TTGAGGGTCAAAATGTAATTTTTG
1 TT-AGGGTCAAAATGTAATTTTTG
514 AAATGTTTAG
Statistics
Matches: 167, Mismatches: 20, Indels: 21
0.80 0.10 0.10
Matches are distributed among these distances:
85 2 0.01
86 47 0.28
87 69 0.41
88 45 0.27
89 4 0.02
ACGTcount: A:0.32, C:0.05, G:0.27, T:0.36
Consensus pattern (85 bp):
TTAGGGTCAAAATGTAATTTTTGGATGTTCGAGGGCAAAATGTAATTTTTGGAAGTTTAGGGGTA
AAATGGTAATTTTGAAAAGT
Found at i:399 original size:29 final size:30
Alignment explanation
Indices: 209--555 Score: 212
Period size: 29 Copynumber: 11.9 Consensus size: 30
199 TTTGAGGGTG
* *
209 AAATGGTACTTTTTGGATA-CTTAGGGG-CA
1 AAATGGTAATTTTTGGA-AGTTTAGGGGTCA
* * *
238 AAATGATAATTTTTGGATGATT-GGGG-CA
1 AAATGGTAATTTTTGGAAGTTTAGGGGTCA
* * * *
266 AAATGGTAATTTTTGGATG-CTCGGGGGCA
1 AAATGGTAATTTTTGGAAGTTTAGGGGTCA
*
295 AAATGGTAA-TTTTGAAAAGTTTA-GGGTCA
1 AAATGGTAATTTTTG-GAAGTTTAGGGGTCA
* *
324 AAATGGTAATTTTTGGATG-TTCGAGGG-CAA
1 AAATGGTAATTTTTGGAAGTTTAG-GGGTC-A
*
354 AAAT-GTGATTTTTGGAAGTTTAGGGGT-A
1 AAATGGTAATTTTTGGAAGTTTAGGGGTCA
* *
382 AAATGGTAATTTTTGGAAAGTTCA-TGGTCA
1 AAATGGTAATTTTTGG-AAGTTTAGGGGTCA
* *
412 AAAT-GTAA-GTTTGTGAAGTTCA-GGGTCA
1 AAATGGTAATTTTTG-GAAGTTTAGGGGTCA
*
440 AAAT-GTAATTTTTAGAAAGTTTAGGGGTCA
1 AAATGGTAATTTTT-GGAAGTTTAGGGGTCA
* **
470 AAAT-GTATTTTTTTTAAAGTTT-GAGGGTCA
1 AAATGGTA-ATTTTTGGAAGTTTAG-GGGTCA
* * *
500 AAAT-GTAATTTTTGAAATGTTTAGAGGTGA
1 AAATGGTAATTTTTGGAA-GTTTAGGGGTCA
* * *
530 AAA-CGTGATTTTTGGATAGTTCAGGG
1 AAATGGTAATTTTTGGA-AGTTTAGGG
556 ACCTTTTGGG
Statistics
Matches: 259, Mismatches: 35, Indels: 47
0.76 0.10 0.14
Matches are distributed among these distances:
27 1 0.00
28 64 0.25
29 98 0.38
30 89 0.34
31 7 0.03
ACGTcount: A:0.31, C:0.05, G:0.27, T:0.36
Consensus pattern (30 bp):
AAATGGTAATTTTTGGAAGTTTAGGGGTCA
Found at i:1914 original size:6 final size:7
Alignment explanation
Indices: 1897--1921 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1887 ATAATAAATC
1897 TTTTTTA
1 TTTTTTA
1904 TTTTTTA
1 TTTTTTA
1911 TTTTTTA
1 TTTTTTA
1918 TTTT
1 TTTT
1922 GTGGTTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:3354 original size:17 final size:17
Alignment explanation
Indices: 3328--3402 Score: 64
Period size: 17 Copynumber: 4.2 Consensus size: 17
3318 TTGATTTTTT
3328 AATTTAAATTTATCTTA
1 AATTTAAATTTATCTTA
*
3345 AATTTGAATTTATCTTTTTA
1 AATTTAAATTTATC---TTA
* *
3365 AATTTAAGTTTGGT-TTA
1 AATTTAAATTT-ATCTTA
3382 AATTTAAATTTAAT-TTA
1 AATTTAAATTT-ATCTTA
3399 AATT
1 AATT
3403 GACTTAAGAT
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
17 34 0.72
20 12 0.26
21 1 0.02
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (17 bp):
AATTTAAATTTATCTTA
Found at i:3363 original size:37 final size:37
Alignment explanation
Indices: 3312--3393 Score: 98
Period size: 37 Copynumber: 2.3 Consensus size: 37
3302 TTAAGTTGGG
*
3312 TTTAAATTGAT-TTTTT-AATTTAAATTT-ATCTTAAA
1 TTTAAATTTATCTTTTTAAATTTAAATTTGAT-TTAAA
* * *
3347 TTTGAATTTATCTTTTTAAATTTAAGTTTGGTTTAAA
1 TTTAAATTTATCTTTTTAAATTTAAATTTGATTTAAA
3384 TTTAAATTTA
1 TTTAAATTTA
3394 ATTTAAATTG
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
35 9 0.23
36 5 0.13
37 24 0.62
38 1 0.03
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.57
Consensus pattern (37 bp):
TTTAAATTTATCTTTTTAAATTTAAATTTGATTTAAA
Found at i:3396 original size:11 final size:11
Alignment explanation
Indices: 3325--3402 Score: 51
Period size: 11 Copynumber: 7.2 Consensus size: 11
3315 AAATTGATTT
3325 TTTAATTTAAA
1 TTTAATTTAAA
3336 TTT-ATCTTAAA
1 TTTAAT-TTAAA
3347 TTTGAATTT--A
1 TTT-AATTTAAA
3357 TCTT--TTTAAA
1 T-TTAATTTAAA
**
3367 TTTAAGTTT-GG
1 TTTAA-TTTAAA
3378 TTTAAATTTAAA
1 TTT-AATTTAAA
3390 TTTAATTTAAA
1 TTTAATTTAAA
3401 TT
1 TT
3403 GACTTAAGAT
Statistics
Matches: 52, Mismatches: 4, Indels: 22
0.67 0.05 0.28
Matches are distributed among these distances:
8 3 0.06
9 2 0.04
10 6 0.12
11 29 0.56
12 10 0.19
13 2 0.04
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:4111 original size:3 final size:3
Alignment explanation
Indices: 4103--4161 Score: 100
Period size: 3 Copynumber: 19.7 Consensus size: 3
4093 AATAAGGCTT
**
4103 TAA TAA TAA TAA TGG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4151 TAA TAA TAA TA
1 TAA TAA TAA TA
4162 TTACTAATAT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:5245 original size:29 final size:28
Alignment explanation
Indices: 5208--5674 Score: 465
Period size: 29 Copynumber: 16.0 Consensus size: 28
5198 GGAGGTCCCT
5208 AAACTTCCAAAAATTCCATTTTTACCCTC
1 AAACTTCCAAAAATTCCATTTTTACCC-C
* ** *
5237 GAACTTCCAAAAACCCCATTTTAACCCC
1 AAACTTCCAAAAATTCCATTTTTACCCC
5265 AAAACTTCCAAAAATTCCATTTTTACCCTC
1 -AAACTTCCAAAAATTCCATTTTTACCC-C
*
5295 GAACTTCCAAAAA-TCTCATTTTTAACCCC
1 AAACTTCCAAAAATTC-CATTTTT-ACCCC
* *
5324 AAAACTCCCAAAAATTCCATTTTCACCCCC
1 -AAACTTCCAAAAATTCCATTTTTA-CCCC
5354 AAACTTCCAAAAATTCCATTTTTACCCC
1 AAACTTCCAAAAATTCCATTTTTACCCC
* * *
5382 TAAACTTCCAAAAATCCCATTTTAACCCTA
1 -AAACTTCCAAAAATTCCATTTTTACCC-C
*
5412 AAACTCCCAAAAATTCCATTTTTACCCC
1 AAACTTCCAAAAATTCCATTTTTACCCC
* *
5440 TGAACTTCCAAAAATTTCATTTTTACCCAC
1 -AAACTTCCAAAAATTCCATTTTTACCC-C
** * *
5470 AAACTTCTTAAAATCCCATTTTAAACCCC
1 AAACTTCCAAAAATTCCATTTT-TACCCC
*
5499 AAAATTTCCAAAAATTCCA-TTTTACCCC
1 -AAACTTCCAAAAATTCCATTTTTACCCC
* **
5527 TAAACTTCCAAAAA-TCTCGTTTTTAATCCTG
1 -AAACTTCCAAAAATTC-CATTTTT-A-CCCC
*
5558 AAACTTCTAAAAA-TCACATTTTTAACCCC
1 AAACTTCCAAAAATTC-CATTTTT-ACCCC
*
5587 GAAACTTCCAAAAATTCTATTTTTACCCTC
1 -AAACTTCCAAAAATTCCATTTTTACCC-C
* * *
5617 GAACTTCCAAAAATTCCATATTTGACCTCA
1 AAACTTCCAAAAATTCCAT-TTTTACC-CC
5647 AAACTTCCAAAAATTCCATTTTTACCCC
1 AAACTTCCAAAAATTCCATTTTTACCCC
5675 CGAATGTCTA
Statistics
Matches: 362, Mismatches: 54, Indels: 45
0.79 0.12 0.10
Matches are distributed among these distances:
27 2 0.01
28 26 0.07
29 216 0.60
30 111 0.31
31 7 0.02
ACGTcount: A:0.36, C:0.31, G:0.02, T:0.31
Consensus pattern (28 bp):
AAACTTCCAAAAATTCCATTTTTACCCC
Found at i:5422 original size:117 final size:117
Alignment explanation
Indices: 5208--5675 Score: 518
Period size: 117 Copynumber: 4.0 Consensus size: 117
5198 GGAGGTCCCT
* * *
5208 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAACCCCATTTTAACCCCAAAACTTC
1 AAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTAACCCCAAAACTTC
* **
5273 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAA-TCTCATTTTTAACCCCA
66 CAAAAATTCCATTTTAACCCTAAAACTTCCAAAAATTC-CATTTTTAACCCCA
* * * * *
5325 AAACTCCCAAAAATTCCATTTTCACCCCCAAACTTCCAAAAATTCCATTTTTACCCCTAAACTTC
1 AAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTAACCCCAAAACTTC
* * *
5390 CAAAAATCCCATTTTAACCCTAAAACTCCCAAAAATTCCATTTTT-ACCCCT
66 CAAAAATTCCATTTTAACCCTAAAACTTCCAAAAATTCCATTTTTAACCCCA
* * * ** *
5441 GAACTTCCAAAAATTTCATTTTTACCCACAAACTTCTTAAAATCCCATTTTAAACCCCAAAATTT
1 AAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTT-AACCCCAAAACTT
* * * **
5506 CCAAAAATTCCATTTTACCCCT-AAACTTCCAAAAA-TCTCGTTTTTAATCCTG
65 CCAAAAATTCCATTTTAACCCTAAAACTTCCAAAAATTC-CATTTTTAACCCCA
* * * * * *
5558 AAACTTCTAAAAA-TCACATTTTTAACCCCGAAACTTCCAAAAATTCTATTTTTACCCTC-GAAC
1 AAACTTCCAAAAATTC-CATTTTT-ACCCCCAAACTTCCAAAAATCCCATTTTAACCC-CAAAAC
* *
5621 TTCCAAAAATTCCATATTTGA-CCTCAAAACTTCCAAAAATTCCATTTTTACCCCC
63 TTCCAAAAATTCCAT-TTTAACCCT-AAAACTTCCAAAAATTCCATTTTTAACCCC
5676 GAATGTCTAA
Statistics
Matches: 290, Mismatches: 50, Indels: 20
0.81 0.14 0.06
Matches are distributed among these distances:
115 2 0.01
116 67 0.23
117 169 0.58
118 28 0.10
119 22 0.08
120 2 0.01
ACGTcount: A:0.36, C:0.31, G:0.02, T:0.31
Consensus pattern (117 bp):
AAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCAAAAATCCCATTTTAACCCCAAAACTTC
CAAAAATTCCATTTTAACCCTAAAACTTCCAAAAATTCCATTTTTAACCCCA
Done.